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Method: Integrating SNVs and CNAs on a phylogenetic tree from single-cell DNA sequencing data
- Liting Zhang,
- Hank W. Bass,
- Jerome Irianto,
- and Xian Mallory
Genome Res. November 2023 33: 2002-2017; Published in Advance November 22, 2023, doi:10.1101/gr.277249.122
...sampled cells together for sequencing, does not differentiate subclones from each other directly (Williams et al. 2018).Single-cell DNA sequencing (scDNA-seq) technologies make it possible to decipher ITH by sequencing one cell at a time (Navin et al. 2011). However, because of the limited quantity of ∼6...
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Method: PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data
- Salem Malikic,
- Farid Rashidi Mehrabadi,
- Simone Ciccolella,
- Md. Khaledur Rahman,
- Camir Ricketts,
- Ehsan Haghshenas,
- Daniel Seidman,
- Faraz Hach,
- Iman Hajirasouliha,
- and S. Cenk Sahinalp
Genome Res. November 2019 29: 1860-1877; Published in Advance October 18, 2019, doi:10.1101/gr.234435.118
...due to the high false negative rates observed in single-cell sequencing. (The relocation of only one single-cell as a result of the high false negative rate may result in very high RF distance.) As a result, RF distance is not commonly used in tumor evolution studies (with the exception of Zafar et al...
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Method: Quantification of somatic mutation flow across individual cell division events by lineage sequencing
- Yehuda Brody,
- Robert J. Kimmerling,
- Yosef E. Maruvka,
- David Benjamin,
- Juniper J. Elacqua,
- Nicholas J. Haradhvala,
- Jaegil Kim,
- Kent W. Mouw,
- Kristjana Frangaj,
- Amnon Koren,
- Gad Getz,
- Scott R. Manalis,
- and Paul C. Blainey
Genome Res. December 2018 28: 1901-1918; Published in Advance November 20, 2018, doi:10.1101/gr.238543.118
...call sets with resolution as high as the single-cell level in subject lineages. Lineage sequencing entails sampling single cells from a population and sequencing subclonal sample sets derived from these cells such that knowledge of relationships among the cells can be used to jointly call variants...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
...-pass whole- sequencing to determine the extent of the copy number alterations exhibited by the proband. The deletion spanned from the telomere of Chromosome 8p to position 7,247,573 (∼7.2 Mb) and encompassed 23 protein-coding genes, whereas the duplication spanned from position 11,828,865–40,361,770 (∼28...
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Method: Marker-free characterization of full-length transcriptomes of single live circulating tumor cells
- Sarita Poonia,
- Anurag Goel,
- Smriti Chawla,
- Namrata Bhattacharya,
- Priyadarshini Rai,
- Yi Fang Lee,
- Yoon Sim Yap,
- Jay West,
- Ali Asgar Bhagat,
- Juhi Tayal,
- Anurag Mehta,
- Gaurav Ahuja,
- Angshul Majumdar,
- Naveen Ramalingam,
- and Debarka Sengupta
Genome Res. January 2023 33: 80-95; Published in Advance November 22, 2022, doi:10.1101/gr.276600.122
...detection methods based on single-cell RNA sequencing (scRNA-seq) use a mix of size selection, marker-based white blood cell (WBC) depletion, and antibodies targeting tumor-associated antigens. However, the majority of these methods either miss out on atypical CTCs or suffer from WBC contamination. We...
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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...a reliable and quantitative understanding of the alterations of genomic structures under different cellular conditions. The genomic structure yielded by CTG serves as an architectural blueprint of the dynamic gene regulatory network, based on which cell-specific correspondence between gene...
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Method: A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y
- Marta Tomaszkiewicz,
- Samarth Rangavittal,
- Monika Cechova,
- Rebeca Campos Sanchez,
- Howard W. Fescemyer,
- Robert Harris,
- Danling Ye,
- Patricia C.M. O'Brien,
- Rayan Chikhi,
- Oliver A. Ryder,
- Malcolm A. Ferguson-Smith,
- Paul Medvedev,
- and Kateryna D. Makova
Genome Res. April 2016 26: 530-540; Published in Advance March 2, 2016, doi:10.1101/gr.199448.115
...obtained 12.5 and 20 million pairs of reads for PE and MP data sets, respectively, that were used in subsequent steps. Next, the PE reads were assembled into contigs using the SPAdes assembler (Bankevich et al. 2012). The initial development of SPAdes focused on single-cell sequencing data. As a result...
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Method: Characterization of network hierarchy reflects cell state specificity in genome organization
- Jingyao Wang,
- Yue Xue,
- Yueying He,
- Hui Quan,
- Jun Zhang,
- and Yi Qin Gao
Genome Res. February 2023 33: 247-260; Published in Advance February 24, 2023, doi:10.1101/gr.277206.122
...are negatively correlated with transcription alteration (Fig. 7A), validating the repressive impacts of H3K27me3-rich loci via physical interactions. To control for variability related to copy number variants (CNVs), we identified significantly changed contacts for genomic regions with rare CNV occurrence (see...
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Research: Mutational bias in spermatogonia impacts the anatomy of regulatory sites in the human genome
- Vera B. Kaiser,
- Lana Talmane,
- Yatendra Kumar,
- Fiona Semple,
- Marie MacLennan,
- Deciphering Developmental Disorders Study,
- David R. FitzPatrick,
- Martin S. Taylor,
- and Colin A. Semple
Genome Res. November 2021 31: 1994-2007; Published in Advance August 20, 2021, doi:10.1101/gr.275407.121
...in spermatogonia, potentially altering neurodevelopmental regulatory architecture. Local chromatin structure in spermatogonia is thus pervasive in shaping both evolution and disease.Mutation is the ultimate source of genetic variation, and inherited variation must invariably arise in the germline. It is well...
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Method: Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations
- Jonathan S. Brammeld,
- Mia Petljak,
- Inigo Martincorena,
- Steven P. Williams,
- Luz Garcia Alonso,
- Alba Dalmases,
- Beatriz Bellosillo,
- Carla Daniela Robles-Espinoza,
- Stacey Price,
- Syd Barthorpe,
- Patrick Tarpey,
- Constantine Alifrangis,
- Graham Bignell,
- Joana Vidal,
- Jamie Young,
- Lucy Stebbings,
- Kathryn Beal,
- Michael R. Stratton,
- Julio Saez-Rodriguez,
- Mathew Garnett,
- Clara Montagut,
- Francesco Iorio,
- and Ultan McDermott
Genome Res. April 2017 27: 613-625; Published in Advance February 8, 2017, doi:10.1101/gr.213546.116
...the mutation spectrum of ENU to that of another mutagen, namely gamma irradiation. Two cancer cell lines (MSI versus MSS) were irradiated, and single cells were expanded to clones prior to exome sequencing.We observed that themutationspectrumdifferedquite significantly for the two cell lines, suggesting...
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